Sequence- and chain-length-specific complementary double-helix formation

Duplex-forming oligocarbamates with tunable nonbonding sites

In biopolymers such as proteins and nucleic acids, monomer sequence encodes for highly specific intra- and intermolecular interactions that direct self-assembly into complex architectures with high fidelity. This remarkable structural control translates into precise control over the properties of the biopolymer. Polymer scientists have sought to achieve similarly precise control over the structure and function of synthetic assemblies. A common strategy for achieving this goal has been to exploit existing biopolymers, known to associate with specific geometries and stoichiometries, for the assembly of synthetic building blocks. However, such systems are neither scalable nor amenable to the relatively harsh conditions required by various materials science applications, particularly those involving non-aqueous environments. To overcome these limitations, we have synthesized sequence-defined oligocarbamates (SeDOCs) that assemble into duplexes through complementary hydrogen bonds between thymine (T) and diaminotriazine (D) pendant groups. The SeDOC platform makes it simple to incorporate non-hydrogen-bonding sites into an oligomer's array of recognition motifs, thereby enabling an investigation into this unexplored handle for controlling the hybridization of complementary ligands. We successfully synthesized monovalent, divalent, and trivalent SeDOCs and characterized their self-assembly via diffusion ordered spectroscopy, 1H-NMR titration, and isothermal titration calorimetry. Our findings reveal that the binding strength of monovalent oligomers with complementary pendant groups is entropically driven and independent of monomer sequence. The results further show that the hybridization of multivalent oligomers is cooperative, that their binding enthalpy (ΔH) and entropy (TΔS) depend on monomer sequence, and that sequence-dependent changes in ΔH and TΔS occur in tandem to minimize the overall change in binding free energy.

Synthetically encoded complementary oligomers

Creating the next generation of advanced materials will require controlling molecular architecture to a degree typically achieved only in biopolymers. Sequence-defined polymers take inspiration from biology by using chain length and monomer sequence as handles for tuning structure and function. These sequence-defined polymers can assemble into discrete structures, such as molecular duplexes, via reversible interactions between functional groups. Selectivity can be attained by tuning the monomer sequence, thereby creating the need for chemical platforms that can produce sequence-defined polymers at scale. Developing sequence-defined polymers that are specific for their complementary sequence and achieve their desired binding strengths is critical for producing increasingly complex structures for new functional materials. In this Review Article, we discuss synthetic platforms that produce sequence-defined, duplex-forming oligomers of varying length, strength and association mode, and highlight several analytical techniques used to characterize their hybridization.

High-Affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water

We prepared a series of water-soluble aromatic oligoamide sequences all composed of a segment prone to form a single helix and a segment prone to dimerize into a double helix. These sequences exclusively assemble as antiparallel duplexes. The modification of the duplex inner rim by varying the nature of the substituents borne by the aromatic monomers allowed us to identify sequences that can hybridize by combining two chemically different strands, with high affinity and complete selectivity in water. X-ray crystallography confirmed the expected antiparallel configuration of the duplexes whereas NMR spectroscopy and mass spectrometry allowed us to assess precisely the extent of the hybridization. The hybridization kinetics of the aromatic strands was shown to depend on both the nature of the substituents responsible for strand complementarity and the length of the aromatic strand. These results highlight the great potential of aromatic hetero-duplex as a tool to construct non-symmetrical dynamic supramolecular assemblies.

Replication of synthetic recognition-encoded oligomers by ligation of trimer building blocks

The development of methods for replication of synthetic information oligomers will underpin the use of directed evolution to search new chemical space. Template-directed replication of triazole oligomers has been achieved using a covalent primer in conjunction with non-covalent binding of complementary building blocks. A phenol primer equipped with an alkyne was first attached to a benzoic recognition unit on a mixed sequence template via selective covalent ester base-pair formation. The remaining phenol recognition units on the template were then used for non-covalent binding of phosphine oxide oligomers equipped with an azide. The efficiency of the templated CuAAC reaction between the primer and phosphine oxide building blocks was investigated as a function of the number of H-bonds formed with the template. Increasing the strength of the non-covalent interaction between the template and the azide lead to a significant acceleration of the templated reaction. For shorter phosphine oxide oligomers intermolecular reactions compete with the templated process, but quantitative templated primer elongation was achieved with a phosphine oxide 3-mer building block that was able to form three H-bonds with the template. NMR spectroscopy and molecular models suggest that the template can fold, but addition of the phosphine oxide 3-mer leads to a complex with three H-bonds between phosphine oxide and phenol groups, aligning the azide and alkyne groups in a favourable geometry for the CuAAC reaction. In the product duplex, 1H and 31P NMR data confirm the presence of the three H-bonded base-pairs, demonstrating that the covalent and non-covalent base-pairs are geometrically compatible. A complete replication cycle was carried out starting from the oligotriazole template by covalent attachment of the primer, followed by template-directed elongation, and hydrolysis of the the ester base-pair in the resulting duplex to regenerate the template and liberate the copy strand. We have previously demonstrated sequence-selective oligomer replication using covalent base-pairing, but the trimer building block approach described here is suitable for replication of sequence information using non-covalent binding of the monomer building blocks to a template.

Recognition-Encoded Synthetic Information Molecules

ConspectusNucleic acids represent a unique class of highly programmable molecules, where the sequence of monomer units incorporated into the polymer chain can be read through duplex formation with a complementary oligomer. It should be possible to encode information in synthetic oligomers as a sequence of different monomer units in the same way that the four different bases program information into DNA and RNA. In this Account, we describe our efforts to develop synthetic duplex-forming oligomers composed of sequences of two complementary recognition units that can base-pair in organic solvents through formation of a single H-bond, and we outline some general guidelines for the design of new sequence-selective recognition systems.The design strategy has focused on three interchangeable modules that control recognition, synthesis, and backbone geometry. For a single H-bond to be effective as a base-pairing interaction, very polar recognition units, such as phosphine oxide and phenol, are required. Reliable base-pairing in organic solvents requires a nonpolar backbone, so that the only polar functional groups present are the donor and acceptor sites on the two recognition units. This criterion limits the range of functional groups that can be produced in the synthesis of oligomers. In addition, the chemistry used for polymerization should be orthogonal to the recognition units. Several compatible high yielding coupling chemistries that are suitable for the synthesis of recognition-encoded polymers are explored. Finally, the conformational properties of the backbone module play an important role in determining the supramolecular assembly pathways that are accessible to mixed sequence oligomers.Almost all complementary homo-oligomers will form duplexes provided the product of the association constant for formation of a base-pair and the effective molarity for the intramolecular base-pairing interactions that zip up the duplex is significantly greater than one. For these systems, the structure of the backbone does not play a major role, and the effective molarities for duplex formation tend to fall in the range 10-100 mM for both rigid and flexible backbones. For mixed sequences, intramolecular H-bonding interactions lead to folding. The competition between folding and duplex formation depends critically on the conformational properties of the backbone, and high-fidelity sequence-selective duplex formation is only observed for backbones that are sufficiently rigid to prevent short-range folding between bases that are close in sequence. The final section of the Account highlights the prospects for functional properties, other than duplex formation, that might be encoded with sequence.

Double helices of dissymmetrical α,α'-disubstituted tripyrrins

Dissymmetrical α,α'-disubstituted tripyrrins have been prepared using a modified synthetic protocol. Tripyrrin 2a bearing 3,5-bis(trifluoromethyl)phenyl and 4-methoxyphenyl moieties showed an anti-type dimer arrangement in the solid state. In contrast, syn-type dimers were observed for tripyrrin 2b bearing 3,5-bis(trifluoromethyl)phenyl and 3,5-di-t-butylphenyl moieties. In addition, proton-exchange NH tautomerization was observed in 2b.

Macromolecular Information Transfer

Macromolecular information transfer can be defined as the process by which a coded monomer sequence is communicated from one macromolecule to another. In such a transfer process, the information sequence can be kept identical, transformed into a complementary sequence or even translated into a different molecular language. Such mechanisms are crucial in biology and take place in DNA→DNA replication, DNA→RNA transcription and RNA→protein translation. In fact, there would be no life on Earth without macromolecular information transfer. Mimicking such processes with synthetic macromolecules would also be of major scientific relevance because it would open up new avenues for technological applications (e.g. data storage and processing) but also for the creation of artificial life. In this important context, this minireview summarizes recent research about information transfer in synthetic oligomers and polymers. Medium- and long-term perspectives are also discussed.

Folding and Duplex Formation in Sequence-Defined Aniline Benzaldehyde Oligoarylacetylenes

In all known genetic polymers, molecular recognition via hydrogen bonding between complementary subunits underpins their ability to encode and transmit information, to form sequence-defined duplexes, and to fold into catalytically active forms. Reversible covalent interactions between complementary subunits provide a different way to encode information, and potentially function, in sequence-defined oligomers. Here, we examine six oligoarylacetylene trimers composed of aniline and benzaldehyde subunits. Four of these trimers self-pair to form two-rung duplex structures, and two form macrocyclic 1,3-folded structures. The equilibrium proportions of these structures can be driven to favor each of the observed structures almost entirely depending upon the concentration of trimers and an acid catalyst. Quenching the acidic trimer solutions with an organic base kinetically traps all species such that they can be isolated and characterized. Mixtures of complementary trimers form exclusively sequence-specific 3-rung duplexes. Our results suggest that reversible covalent bonds could in principle guide the formation of more complex folded conformations of longer oligomers.

Substituent Effects at the 5,10-Positions of Dianilinotripyrrins on Their Dimerization Themodynamics

Control of the association behavior by the molecular design is one of the most essential benefits in artificial supramolecular systems. 1,14-Dianilinotripyrrin has recently emerged as a novel conjugated molecule which forms a double helix in non-polar solvents with the aid of multiple interstrand hydrogen bonding interactions. In this work, we investigated the substituent effects at the 5,10-positions of tripyrrin on their association thermodynamics. This study illuminated two key findings; 1) electronic tuning by the para-substituents reduce the entropic costs thereby slightly improve the association constants, and 2) ortho-substituents force the tripyrrin core to be relatively planar, which significantly decrease the association constant due to less feasible π-stacking.

Functional Chirality: From Small Molecules to Supramolecular Assemblies

Many structures in nature look symmetric, but this is not completely accurate, because absolute symmetry is close to death. Chirality (handedness) is one form of living asymmetry. Chirality has been extensively investigated at different levels. Many rules were coined in attempts made for many decades to have control over the selection of handedness that seems to easily occur in nature. It is certain that if good control is realized on chirality, the roads will be ultimately open towards numerous developments in pharmaceutical, technological, and industrial applications. This tutorial review presents a report on chirality from single molecules to supramolecular assemblies. The realized functions are still in their infancy and have been scarcely converted into actual applications. This review provides an overview for starters in the chirality field of research on concepts, common methodologies, and outstanding accomplishments. It starts with an introductory section on the definitions and classifications of chirality at the different levels of molecular complexity, followed by highlighting the importance of chirality in biological systems and the different means of realizing chirality and its inversion in solid and solution-based systems at molecular and supramolecular levels. Chirality-relevant important findings and (bio-)technological applications are also reported accordingly.

Controlling the helicity of π-conjugated oligomers by tuning the aromatic backbone twist

The properties of π-conjugated oligomers and polymers are commonly controlled by side group engineering, main chain engineering, or conformational engineering. The last approach is typically limited to controlling the dihedral angle around the interring single bonds to prevent loss of π-conjugation. Here we propose a different approach to conformational engineering that involves controlling the twist of the aromatic units comprising the backbone by using a tether of varying lengths. We demonstrate this approach by synthesizing an inherently twisted building unit comprised of helically locked tethered acenes, bearing acetylene end-groups to enable backbone extension, which was applied in a series of nine helical oligomers with varying backbone length and twist. We find that the optical and electronic properties of π-conjugated systems may be determined by the additive, antagonistic, or independent effects of backbone length and twist angle. The twisted oligomers display chiral amplification, arising from the formation of secondary helical structures.

One approach to altering the properties of π-conjugated oligomers is conformational engineering, in which the degree of rotation around the bonds linking monomers is restricted. Here the authors apply the conformational engineering approach on individual monomers using tethers of varying lengths to twist the aromatic units, and study the effects of varying the angles.

Four- and two-armed hetero porphyrin dimers: their specific recognition and self-sorting behaviours

In this study we self-assembled the four-armed porphyrin hetero dimer capsule Cap4, stabilized through amidinium-carboxylate salt bridges, in CH₂Cl₂ and CHCl₃. The dimer capsule Cap4 was kinetically and thermodynamically more stable than the corresponding two-armed dimer Cap2. The number of arms strongly influenced their recognition behaviour; guests possessing small aromatic faces (e.g., 1,3,5-trinitrobenzene) preferred residing in the cavity of the two-armed capsule Cap2, rather than in Cap4, both thermodynamically and kinetically; in contrast, large aromatic guests (e.g., 9,10-dibromoanthracene) were encapsulated predominantly by Cap4 because of favourable entropic effects. The number of arms enabled self-sorting behaviour of the dimer formation; complexation studies using an equimolar mixture of the four porphyrin constituents of the two capsules revealed the quantitative formation of the corresponding dimers Cap2 and Cap4. Furthermore, we examined the specific molecular recognition of Cap2 and Cap4; NMR experiments of mixtures of Cap2 and Cap4 in the presence of favourable guests for Cap2 and Cap4 revealed that these guest molecules were encapsulated selectively by their preferred hosts.

A peptidomimetic-based thixotropic organogel showing syneresis-induced anti-adhesion against water and ice

A peptidomimetic containing 2,6-dimethylpyridine-3,5-dicarboxylic acid and phenylalanine formed a thixotropic gel which shows syneresis under appropriate conditions and anti-adhesion against water and ice.

Versatility in Self-assembly and Morphology of Non-Coded Anthranilic acid and Phenylglycine based Dipeptide Stereoisomers

Beauty in the self-assembly patterns of isomeric dipeptides of Boc-Ant-L-Phg-OMe (1) bearing two rigid, unnatural amino acids (Ant: Anthranilic acid, Phg: Phenylglycine) is demonstrated. Additionally, self-assembly and morphological variation by...

Duplex vs. folding: tuning the self-assembly of synthetic recognition-encoded aniline oligomers

One of the challenges in the realization of synthetic oligomers capable of sequence-selective duplex formation is intramolecular folding interaction between complementary recognition units. To assess whether complementary hetero-oligomers can assemble into high fidelity duplex structures, the competing folding equilibria must be carefully considered. A family of recognition-encoded aniline oligomers were assembled via reductive amination of dianiline linkers and dialdehyde monomers, which were equipped with either a 2-trifluoromethylphenol or a phosphine oxide H-bond recognition unit. To test the possibility of 1,2-folding in mixed sequence oligomers, the self-assembly properties of the homo- and hetero-dimers were characterised by ¹⁹F and ¹H NMR titration and dilution experiments in toluene and in chloroform. Three different systems were investigated with variations in the steric bulk around the H-bond acceptor unit and the length of the dianiline linker. For two systems, the hetero-dimers folded with intramolecular H-bonding in the monomeric state, reducing stability of the intermolecular duplex by two to three orders of magnitude compared with the corresponding homo-oligomers. However, the use of a long rigid linker as the backbone connecting two monomer units successfully prevents 1,2-folding and leads to the formation of a stable mixed sequence duplex in toluene.

A supramolecular double-helix based on complementary phosphate-guanidinium pairing

A double-helical supramolecular structure was formed by self-assembly of 1,1'-binaphthyl-based bisguanidines and bisphosphoric acids. Interestingly the homochiral (S,S) + (S,S)-pair forms a left-handed double-helix, while the heterochiral (S,S) + (R,R)-pair forms a non-helical dimer.

Symmetry breaking-induced double-strand helices in H-bonded coassembly

Double-strand helical structures are important in information storage of biomacromolecules, while the artificial synthesis depends on chirality transfer from the molecular to supramolecular scale, and the synthesis through symmetry breaking has yet been accomplished. In this work, we present the multiple-constituent coassembly of a melamine derivative and an N-terminal aromatic amino acid into double helical nanoarchitectures via symmetry breaking. Multiple intramolecular H-bond formation between constituents played key roles in directing the formation of helical structures. Intertwining of single helices with identical helical parameters afforded double helical structures, benefiting from the uniformity and monodispersity of nanoarchitectures. With introduction of coded chiral amino acid derivatives as chiral sources, the handedness could be readily manipulated with exclusive correlation to the absolute chirality of amino acids. Molecular flexibility of the melamine derivative facilitates the propeller-shaped complex formation to afford helical columnar coassemblies and double helical structures. This work presents a rational control over the emergence and properties of double helical structures in multiple-constituent coassemblies through symmetry breaking, which provides an alternative method towards the synthesis of topological chiral composites and chiroptical materials.

Folding and duplex formation in mixed sequence recognition-encoded m-phenylene ethynylene polymers

Oligomers equipped with complementary recognition units have the potential to encode and express chemical information in the same way as nucleic acids. The supramolecular assembly properties of m-phenylene ethynylene polymers equipped with H-bond donor (D = phenol) and H-bond acceptor (A = phosphine oxide) side chains have been investigated in chloroform solution. Polymerisation of a bifunctional monomer in the presence of a monofunctional chain stopper was used for the one pot synthesis of families of m-phenylene ethynylene polymers with sequences ADnA or DAnD (n = 1-5), which were separated by chromatography. All of the oligomers self-associate due to intermolecular H-bonding interactions, but intramolecular folding of the monomeric single strands can be studied in dilute solution. NMR and fluorescence spectroscopy show that the 3-mers ADA and DAD do not fold, but there are intramolecular H-bonding interactions for all of the longer sequences. Nevertheless, 1 : 1 mixtures of sequence complementary oligomers all form stable duplexes. Duplex stability was quantified using DMSO denaturation experiments, which show that the association constant for duplex formation increases by an order of magnitude for every base-pairing interaction added to the chain, from 103 M-1 for ADA·DAD to 105 M-1 for ADDDA·DAAAD. Intramolecular folding is the major pathway that competes with duplex formation between recognition-encoded oligomers and limits the fidelity of sequence-selective assembly. The experimental approach described here provides a practical strategy for rapid evaluation of suitability for the development of programmable synthetic polymers.

High-Fidelity Sequence-Selective Duplex Formation by Recognition-Encoded Melamine Oligomers

Melamine oligomers composed of repeating triazine-piperidine units and equipped with phenol and phosphine oxide side-chains form H-bonded duplexes. The melamine backbone provides sufficient rigidity to prevent intramolecular folding of oligomers up to three recognition units in length, leading to reliable duplex formation between sequence complementary oligomers. NMR spectroscopy and isothermal titration calorimetry (ITC) were used to characterize the self-assembly properties of the oligomers. For length-complementary homo-oligomers, duplex formation in toluene is characterized by an increase in stability of an order of magnitude for every base-pair added to the chain. NMR spectra of dilute solutions of the AD 2-mer show that intramolecular H-bonding between neighboring recognition units on the chain (1,2-folding) does not occur. NMR spectra of dilute solutions of both the AAD and the ADD 3-mer show that 1,3-folding does not take place either. ITC was used to characterize interactions between all pairwise combinations of the six different 3-mer sequences, and the sequence complementary duplexes are approximately an order of magnitude more stable than duplexes with a single base mismatch. High-fidelity duplex formation combined with the synthetic accessibility of the monomer building blocks makes these systems attractive targets for further investigation.

Single- and double-helices of α,α'-dibenzylaminotripyrrin: solution and solid state studies

The dimeric association of α,α'-di(benzylamino)tripyrrin in chloroform was found to be 40 times less effective than that of previously reported α,α'-dianilinotripyrrin, which, however, led us to observe the co-crystal structure of single and double helix forms. Attachment of chiral phenylethylamines on the same tripyrrin platform was also performed to induce helical chirality.

Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends

In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.

Metallo-Helicoid with Double Rims: Polymerization Followed by Folding by Intramolecular Coordination

In this study, we established a feasible strategy to construct a new type of metallo-polymer with helicoidal structure through the combination of covalent polymerization and intramolecular coordination-driven self-assembly. In the design, a tetratopic monomer (M) was prepared with two terminal alkynes in the outer rim for polymerization, and two terpyridines (TPYs) in the inner rim for subsequent folding by selective intramolecular coordination. Then, the linear covalent polymer (P) was synthesized by polymerization of M via Glaser-Hay homocoupling reaction. Finally, intramolecular coordination interactions between TPYs and Zn(II) folded the backbone of P into a right- or left-handed metallo-helicoid (H) with double rims. Owing to multiple positive charges on the inner rim of helicoid, double-stranded DNA molecules (dsDNA) could interact with H through electrostatic interactions. Remarkably, dsDNA allowed exclusive formation of H with right handedness by means of chiral induction.

The Diverse World of Foldamers: Endless Possibilities of Self-Assembly

Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.

Supramolecular catalysis by recognition-encoded oligomers: discovery of a synthetic imine polymerase

All key chemical transformations in biology are catalysed by linear oligomers. Catalytic properties could be programmed into synthetic oligomers in the same way as they are programmed into proteins, and an example of the discovery of emergent catalytic properties in a synthetic oligomer is reported. Dynamic combinatorial chemistry experiments designed to study the templating of a recognition-encoded oligomer by the complementary sequence have uncovered an unexpected imine polymerase activity. Libraries of equilibrating imines were formed by coupling diamine linkers with monomer building blocks composed of dialdehydes functionalised with either a trifluoromethyl phenol (D) or phosphine oxide (A) H-bond recognition unit. However, addition of the AAA trimer to a mixture of the phenol dialdehyde and the diamine linker did not template the formation of the DDD oligo-imine. Instead, AAA was found to be a catalyst, leading to rapid formation of long oligomers of D. AAA catalysed a number of different imine formation reactions, but a complementary phenol recognition group on the aldehyde reaction partner is an essential requirement. Competitive inhibition by an unreactive phenol confirmed the role of H-bonding in substrate recognition. AAA accelerates the rate of imine formation in toluene by a factor of 20. The kinetic parameters for this enzyme-like catalysis are estimated as 1 × 10^-3 s^-1 for k _cat and the dissociation constant for substrate binding is 300 μM. The corresponding DDD trimer was found to catalyse oligomerisation the phosphine oxide dialdehyde with the diamine linker, suggesting an important role for the backbone in catalysis. This unexpected imine polymerase activity in a duplex-forming synthetic oligomer suggests that there are many interesting processes to be discovered in the chemistry of synthetic recognition-encoded oligomers that will parallel those found in natural biopolymers.

Self-Assembly of N-Terminal Aryl Amino Acids into Adaptive Single- and Double-Strand Helices

Helical structures are important features of many important biomacromolecules such as double helices and single α-helices in DNA and protein, respectively, yet the self-organization of short oligopeptides (<3) or independent amino acids into artificial helical structures on the atomic level remains mysterious. Here we present the direct construction of artificial double and single helices from N-terminated aryl amino acids (ferrocene phenylalanine (Phe) conjugates) despite both Phe and Phe-Phe dipeptide self-aggregations adopting supramolecular β-sheet structures, which also demonstrated chirality evolution exposed to small molecular binders. In the solid state, the box-shaped building unit stacks into a double helix with enantiomer-resolved handedness driven orthogonally by H-bonds and the CH-π interaction. The entire double helix is noncovalently linked except for the hybridization regions. Asymmetric H-bonds between carboxylic acids and amides facilitates the one-dimensional helical packing of amino acid residues. The ditopic building unit adopts intramolecular H-bonds, facilitating single-strand helix formation. In aqueous self-assemblies, the superhelical structures were retained, which underwent chirality transfer and handedness inversion upon complexation orthogonally by H-bonds and charge-transfer interaction, showing adaptivity to environmental factors.

Ligands with Two Monoanionic N,N-Binding Sites: Synthesis and Coordination Chemistry

Polytopic ligands have become ubiquitous in coordination chemistry because they grant access to a variety of mono- and polynuclear complexes of transition metals as well as rare-earth and main-group elements. Nitrogen-based ditopic ligands, in which two monoanionic N,N-binding sites are framed within one molecule, are of particular importance and are therefore the primary focus of this review. In detail, bis(amidine)s, bis(guanidine)s, bis(β-diimine)s, bis(aminotroponimine)s, bis(pyrrolimine)s, and miscellaneous bis(N,N-chelating) ligands are reviewed. In addition to the general synthetic protocols, the application of these ligands is discussed along with their coordination chemistry, the multifarious binding modes, and the ability of these ligands to bridge two (or more) metal(loids).

Complementary double-stranded helical oligomers bearing achiral bifunctional groups that catalyze asymmetric aldol reaction

Two novel chiral dimer and trimer strands composed of m-terphenyl groups linked through p-diethynylbenzene units with the chiral amidine group and achiral piperazine group introduced at the terminus or center of the strands, respectively, and its complementary achiral carboxylic acid dimer and trimer were synthesized. The complementary chiral/achiral strands form an excess-handed double-helical structure as supported by intense split-type Cotton effects in the absorption regions of the conjugated backbones biased by the chiral amidinium-carboxylate salt bridges. The double-helical trimer was found to catalyze the direct aldol reaction of cyclohexanone with 4-nitrobenzaldehyde and produce the products with a moderate enantioselectivity despite the fact that the catalytically active bifunctional piperazine/carboxylic acid pair introduced in the middle is achiral, indicating the key role of the one-handed double-helical framework for supramolecular bifunctional organocatalysis.

Two-component assembly of recognition-encoded oligomers that form stable H-bonded duplexes

Imine chemistry was used to assemble oligomers displaying phenol and phosphine oxide side chains that selectively base-pair to give duplexes, which are stable in chloroform solution.

A new family of recognition-encoded oligomers that form stable duplexes in chloroform have been prepared. Monomer building blocks composed of dialdehydes functionalised with either a trifluoromethylphenol or phosphine oxide H-bond recognition unit were prepared. The dialdehydes were coupled with diamines by imine formation and then reduction to give homo-oligomers between one and three recognition units in length. Duplex formation was characterised by ¹⁹F and ¹H NMR titration experiments in toluene and in chloroform. For duplexes formed between length complementary H-bond donor and acceptor homo-oligomers, an order of magnitude increase in stability was observed for every base-pair added to the duplex in chloroform. The effective molarity for the intramolecular H-bonds responsible for zipping up the duplex is 30 mM, which results in the fully assembled duplex in all cases. The uniform increase in duplex stability with oligomer length suggests that the backbone structure and geometry is likely to be compatible with the formation of extended duplexes in longer oligomers.

The helix-inversion mechanism in double-stranded helical oligomers bridged by rotary cyclic boronate esters

Attracted by the numerous regulatory functions of double-helical biopolymers such as DNA, many researchers have synthesized various double-helical systems. A recently synthesized double-stranded helical oligomer covalently bridged by rotary boronate esters (BBDD) was shown to undergo helix-inversion that might serve as platform to design rotor systems. However, the detailed helix-inversion mechanism could not be investigated experimentally. Direct molecular dynamics simulations based on density-functional tight-binding energies and gradients computed on-the-fly reveal that disentanglement to the unraveled form and following exchange of the twisted terminal trimethylsilyl (TMS) groups are prerequisites for the observed helix-inversion. The potential of mean force confirms that the originally assumed "concurrent" rotation of the boronate esters and the helix-inversion involves shorter time scale "step-wise" processes, triggered by the disentanglement and exchange of the TMS groups. These results indicate that inversion dynamics of double-helical molecules such as BBDD may be controllable by chemical fine-tuning of the terminal groups. © 2019 Wiley Periodicals, Inc.

Single-handed supramolecular double helix of homochiral bis(N-amidothiourea) supported by double crossed C-I···S halogen bonds

The natural DNA double helix consists of two strands of nucleotides that are held together by multiple hydrogen bonds. Here we propose to build an artificial double helix from fragments of two strands connected by covalent linkages therein, but with halogen bonding as the driving force for self-assembling the fragments to the double helix. We succeed in building such a double helix in both solution and solid state, by using a bilateral N-(p-iodobenzoyl)alanine based amidothiourea which in its folded cis-form allows double and crossed C−I···S halogen bonds that lead to right- or left-handed double helix when the two alanine residues are of the same L,L- or D,D-configuration. The double helix forms in dilute CH₃CN solution of the micromolar concentration level, e.g., 5.6 μM from 2D NOESY experiments and exhibits a high thermal stability in solution up to 75 °C, suggesting cooperative and thereby strong intermolecular double crossed halogen bonding that makes the double helix stable. This is supported by the observed homochiral self-sorting in solution.

Building an artificial double helix is a compelling challenge, and most strategies rely on the intertwining of two helical strands. Here, in a very different approach, the authors construct a supramolecular double helix from multiple synthetic small molecules chained together by double crossed halogen bonds.

Building blocks for recognition-encoded oligoesters that form H-bonded duplexes

A long-short base-pairing scheme hinders intramolecular folding and allows the use of flexible backbones in duplex-forming oligomers.

Competition from intramolecular folding is a major challenge in the design of synthetic oligomers that form intermolecular duplexes in a sequence-selective manner. One strategy is to use very rigid backbones that prevent folding, but this design can prejudice duplex formation if the geometry is not exactly right. The alternative approach found in nucleic acids is to use bases (or recognition units) that have different dimensions. A long-short base-pairing scheme makes folding geometrically difficult and is compatible with the flexible backbones that are required to guarantee duplex formation. A monomer building block equipped with a long hydrogen bond donor (phenol, D) recognition unit and a monomer building block equipped with a short hydrogen bond acceptor (phosphine oxide, A) recognition unit were prepared with differentially protected alcohol and carboxylic acid groups. These compounds were used to synthesise the homo and hetero-sequence 2-mers AA, DD and AD. ¹⁹F and ³¹P NMR experiments were used to characterize the assembly properties of these compounds in toluene solution. AA and DD form a stable doubly-hydrogen-bonded duplex with an effective molarity of 20 mM for formation of the second intramolecular hydrogen bond. AD forms a duplex of similar stability. There is no evidence of intramolecular folding in the monomeric state of this compound, which shows that the long-short base-pairing scheme is effective. The ester coupling chemistry used here is an attractive method for the synthesis of long oligomers, and the properties of the 2-mers indicate that this molecular architecture should give longer mixed sequence oligomers that show high fidelity sequence-selective duplex formation.

Halogen Bonding Directed Supramolecular Quadruple and Double Helices from Hydrogen-Bonded Arylamide Foldamers

Halogen bonding has been used to glue together hydrogen-bonded short arylamide foldamers to achieve new supramolecular double and quadruple helices in the solid state. Three compounds, which bear a pyridine at one end and either a CF₂ I or fluorinated iodobenzene group at the other end, engage in head-to-tail N⋅⋅⋅I halogen bonds to form one-component supramolecular P and M helices, which stack to afford supramolecular double-stranded helices. One of the double helices can dimerize to form a G-quadruplex-like supramolecular quadruple helix. Another symmetric compound, which bears a pyridine at each end, binds to ICF₂ CF₂ I through N⋅⋅⋅I halogen bonds to form two-component supramolecular P and M helices, with one turn consisting of four (2+2) molecules. Half of the pyridine-bearing molecules in two P helices and two M helices stack alternatingly to form another supramolecular quadruple helix. Another half of the pyridine-bearing molecules in such quadruple helices stack alternatingly with counterparts from neighboring quadruple helices, leading to unique quadruple helical arrays in two-dimensional space.

H-Bonded Duplexes based on a Phenylacetylene Backbone

Complementary phenylacetylene oligomers equipped with phenol and phosphine oxide recognition sites form stable multiply H-bonded duplexes in toluene solution. Oligomers were prepared by Sonogashira coupling of diiodobenzene and bis-acetylene building blocks in the presence of monoacetylene chain terminators. The product mixtures were separated by reverse phase preparative high-pressure liquid chromatography to give a series of pure oligomers up to seven recognition units in length. Duplex formation between length complementary homo-oligomers was demonstrated by 31P NMR denaturation experiments using dimethyl sulfoxide as a competing H-bond acceptor. The denaturation experiments were used to determine the association constants for duplex formation, which increase by nearly 2 orders of magnitude for every phenol-phosphine oxide base-pair added. These experiments show that the phenylacetylene backbone supports formation of extended duplexes with multiple cooperative intermolecular H-bonding interactions, and together with previous studies on the mixed sequence phenylacetylene 2-mer, suggest that this supramolecular architecture is a promising candidate for the development of synthetic information molecules that parallel the properties of nucleic acids.

Conjugated double helices via self-dimerization of α,α'-dianilinotripyrrins

A new motif for artificial double helices was developed on the basis of α,α'-disubstituted tripyrrin. α,α'-Dibromotripyrrin 3 was prepared by gentle bromination at the pyrrolic α-positions of 5,10-diphenyltripyrrane followed by oxidation with DDQ. Nucleophilic substitution reactions of 3 with anilines proceeded efficiently to furnish a series of α,α'-dianilinotripyrrins 4-11, which displayed monomeric and dimeric forms depending upon the solvent used for crystallization and the structures of the substituted anilines. Dimeric forms show double helical structures with smooth π-conjugation as indicated by their absorption spectra. van't-Hoff plot analyses revealed that the dimerizations in CDCl3 are enthalpy-driven. Larger association constants of the dimerization are attained for 3,5-di-t-butylanilino- and 3,5-bis(trifluoromethyl)anilino-substituted tripyrrins (7 and 8) via additional multiple intermolecular interactions. In a nonpolar and aprotic solvent, tripyrrins (9 and 10) bearing bulkier 1-naphthylamino and mesitylamino groups do not dimerize but undergo unique tautomerization.

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.

Chiral Template-Directed Regio-, Diastereo-, and Enantioselective Photodimerization of an Anthracene Derivative Assisted by Complementary Amidinium-Carboxylate Salt Bridge Formation

A series of optically active amidine dimers composed of m-terphenyl backbones joined by a variety of linkers, such as achiral and chiral p-phenylene and chiral amide linkers, were synthesized and used as templates for the regio- (head-to-tail (HT) or head-to-head (HH)), diastereo- (anti or syn), and enantioselective [4 + 4] photocyclodimerization of an achiral m-terphenyl-based carboxylic acid monomer bearing a prochiral 2-substituted anthracene at one end (1) through complementary amidinium-carboxylate salt bridges. The amidine dimers linked by p-phenylene linkages almost exclusively afforded the chiral syn-HT and anti-HH dimers at 25 °C, while those joined by amide linkers produced all four dimers. The p-phenylene-linked templates tended to enhance the syn-HT-photodimer formation at high temperatures with no significant changes in the product enantiomeric excess (ee), while the anti-HH-photodimer formation remarkably increased with the decreasing temperature accompanied by a significant enhancement of the product ee up to -86% at -50 °C. Temperature-dependent inversion of the chirality of the anti-HH dimer was observed when the chiral phenylene-linked amidine dimer was used and the product ee was changed from 22% at 50 °C to -86% at -50 °C. A similar enhancement of the enantioselectivity of the anti-HH dimer was also observed for the chiral amide-linked template, producing the anti-HH dimer with up to -88% ee at -50 °C. The observed difference in the regio-, diastereo-, and enantioselectivities due to the difference in the linker structures of the amidine dimers during the template-directed photodimerization of 1 was discussed on the basis of a reversible conformational change in the amidine dimers complexed with 1.

H-Bond Self-Assembly: Folding versus Duplex Formation

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

Homochiral oligomers with highly flexible backbones form stable H-bonded duplexes

Two homochiral building blocks featuring a protected thiol, an alkene and a H-bond recognition unit (phenol or phosphine oxide) have been prepared. Iterative photochemical thiol-ene coupling reactions were used to synthesize oligomers containing 1-4 phosphine oxide and 1-4 phenol recognition sites. Length-complementary H-bond donor and H-bond acceptor oligomers were found to form stable duplexes in toluene. NMR titrations and thermal denaturation experiments show that the association constant and the enthalpy of duplex formation increase significantly for every additional H-bonding unit added to the chain. There is an order of magnitude increase in stability for each additional H-bonding interaction at room temperature indicating that all of the H-bonding sites are fully bound to their complements in the duplexes. The backbone of the thiol-ene duplexes is a highly flexible alkane chain, but this conformational flexibility does not have a negative impact on binding affinity. The average effective molarity for the intramolecular H-bonding interactions that zip up the duplexes is 18 mM. This value is somewhat higher than the EM of 14 mM found for a related family of duplexes, which have the same recognition units but a more rigid backbone prepared using reductive amination chemistry. The flexible thiol-ene AAAA·DDDD duplex is an order of magnitude more stable than the rigid reductive amination AAAA·DDDD duplex. The backbone of the thiol-ene system retains much of its conformational flexibility in the duplex, and these results show that highly flexible molecules can make very stable complexes, provided there is no significant restriction of degrees of freedom on complexation.

Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions

In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.